Genetic predisposition to ocular melanoma

Microdissection of Distinct Morphological Regions Within Uveal Melanomas Identifies Novel Drug Targets

Background/Objectives: Uveal melanomas (UMs) are rare but often deadly malignancies that urgently require viable treatment options. UMs often exhibit tumour heterogeneity, with macroscopic and microscopic differences in morphology between different regions of the same tumour. However, to date, the clinical significance of this and how it may help guide personalised therapy have not been realised. Methods: Using targeted DNA and RNA sequencing of a small case series of large, high-risk primary UMs, we explored whether morphologically distinct regions of the same tumour were associated with distinct molecular profiles. Results: In four of the seven tumours analysed, we detected different sets of genetic variants following the separate analysis of microdissected melanotic and amelanotic regions of the same tumour. These included a MET exon 14 skipping RNA transcript that predicts sensitivity to crizotinib and variants in other genes that are important in active clinical trials for patients with UM and advanced solid tumours. The integration of TCGA data also identified recurrent mutational events in genes that were not previously implicated in UM development (FANCA, SLX4, BRCA2, and ATRX). Conclusions: Our findings show that the molecular analysis of spatially separated and morphologically distinct regions of the same tumour may yield additional, therapeutically relevant genetic variants in uveal melanomas and have implications for the future molecular testing of UMs to identify targeted therapies.

Bilateral Uveal Melanoma: An Insight into Genetic Predisposition in Four New Unrelated Patients and Review of Published Cases

Background: Primary bilateral uveal melanoma (BUM) is an exceptionally rare form of uveal melanoma (UM). This study aimed to explore the potential existence of a genetic predisposition towards the development of BUM. Methods: We employed an exome sequencing approach on germline DNA from four unrelated patients diagnosed with BUM, seeking pathogenic or likely pathogenic variants indicative of a genetic predisposition to UM. Results: None of the patients exhibited pathogenic variants in the BAP1 gene. However, loss-of-function (LoF) variants in the TERF2IP and BAX genes were identified in two of the BUM patients. For patients BUM1 and BUM2, no pathogenic/likely pathogenic variants of significant clinical relevance to BUM were found to warrant inclusion in this report. Conclusions: Our findings suggest the presence of yet-to-be-discovered genes that may contribute to UM predisposition, as evidenced by the absence of pathogenic variants in known UM predisposition genes among the four BUM patients studied. The TERF2IP and BAX genes emerge as noteworthy candidates for further investigation regarding their role in genetic predisposition to UM. Specifically, the potential role of UM as a candidate cancer within the spectrum of cancers linked to pathogenic variants in the TERF2IP gene and other genes associated with the shelterin complex warrants further examination. Additional functional studies are necessary to support or challenge this hypothesis.

The multifunctional human ocular melanocortin system

Immune privilege in the eye involves physical barriers, immune regulation and secreted proteins that together limit the damaging effects of intraocular immune responses and inflammation. The neuropeptide alpha-melanocyte stimulating hormone (α-MSH) normally circulates in the aqueous humour of the anterior chamber and the vitreous fluid, secreted by iris and ciliary epithelium, and retinal pigment epithelium (RPE). α-MSH plays an important role in maintaining ocular immune privilege by helping the development of suppressor immune cells and by activating regulatory T-cells. α-MSH functions by binding to and activating melanocortin receptors (MC1R to MC5R) and receptor accessory proteins (MRAPs) that work in concert with antagonists, otherwise known as the melanocortin system. As well as controlling immune responses and inflammation, a broad range of biological functions is increasingly recognised to be orchestrated by the melanocortin system within ocular tissues. This includes maintaining corneal transparency and immune privilege by limiting corneal (lymph)angiogenesis, sustaining corneal epithelial integrity, protecting corneal endothelium and potentially enhancing corneal graft survival, regulating aqueous tear secretion with implications for dry eye disease, facilitating retinal homeostasis via maintaining blood-retinal barriers, providing neuroprotection in the retina, and controlling abnormal new vessel growth in the choroid and retina. The role of melanocortin signalling in uveal melanocyte melanogenesis however remains unclear compared to its established role in skin melanogenesis. The early application of a melanocortin agonist to downregulate systemic inflammation used adrenocorticotropic hormone (ACTH)-based repository cortisone injection (RCI), but adverse side effects including hypertension, edema, and weight gain, related to increased adrenal gland corticosteroid production, impacted clinical uptake. Compared to ACTH, melanocortin peptides that target MC1R, MC3R, MC4R and/or MC5R, but not adrenal gland MC2R, induce minimal corticosteroid production with fewer amdverse systemic effects. Pharmacological advances in synthesising MCR-specific targeted peptides provide further opportunities for treating ocular (and systemic) inflammatory diseases. Following from these observations and a renewed clinical and pharmacological interest in the diverse biological roles of the melanocortin system, this review highlights the physiological and disease-related involvement of this system within human eye tissues. We also review the emerging benefits and versatility of melanocortin receptor targeted peptides as non-steroidal alternatives for inflammatory eye diseases such as non-infectious uveitis and dry eye disease, and translational applications in promoting ocular homeostasis, for example, in corneal transplantation and diabetic retinopathy.

Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments

MOTIVATION

The ever-growing size of sequencing data is a major bottleneck in bioinformatics as the advances of hardware development cannot keep up with the data growth. Therefore, an enormous amount of data is collected but rarely ever reused, because it is nearly impossible to find meaningful experiments in the stream of raw data.

RESULTS

As a solution, we propose Needle, a fast and space-efficient index which can be built for thousands of experiments in <2 h and can estimate the quantification of a transcript in these experiments in seconds, thereby outperforming its competitors. The basic idea of the Needle index is to create multiple interleaved Bloom filters that each store a set of representative k-mers depending on their multiplicity in the raw data. This is then used to quantify the query.

AVAILABILITY AND IMPLEMENTATION

https://github.com/seqan/needle.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Disparities in Uveal Melanoma: Patient Characteristics

Uveal melanoma is the most common intraocular malignancy in adults. Despite excellent rates of local control, half of all patients with uveal melanoma ultimately go on to develop fatal metastatic disease. This review focuses on disparities and differences in the underlying characteristics of the patients, and how these patient characteristics impact the development of metastasis and subsequent patient survival. Specifically, we detail disparities in epidemiology and risk factors as they relate to the development of primary uveal melanoma, to the development of metastasis, and to patient survival following metastasis.

Hereditary uveal melanoma: a report of a germline mutation in BAP1

Melanoma of the eye is a rare and distinct subtype of melanoma, which only rarely are familial. However, cases of uveal melanoma (UM) have been found in families with mixed cancer syndromes. Here, we describe a comprehensive search for inherited genetic variation in a family with multiple cases of UM but no aggregation of other cancer diagnoses. The proband is a woman diagnosed with UM at 16 years who within 6 months developed liver metastases. We also identified two older paternal relatives of the proband who had died from UM. We performed exome sequencing of germline DNA from members of the affected family. Exome-wide analysis identified a novel loss-of-function mutation in the BAP1 gene, previously suggested as a tumor suppressor. The mutation segregated with the UM phenotype in this family, and we detected a loss of the wild-type allele in the UM tumor of the proband, strongly supporting a causative association with UM. Screening of BAP1 germline mutations in families predisposed for UM may be used to identify individuals at increased risk of disease. Such individuals may then be enrolled in preventive programs and regular screenings to facilitate early detection and thereby improve prognosis.

Molecular pathology of uveal melanoma

Like other cancers, uveal melanomas (UM) are characterised by an uncontrolled, clonal, cellular proliferation, occurring as a result of numerous genetic, and epigenetic aberrations. Signalling pathways known to be disrupted in UM include: (1) the retinoblastoma pathway, probably as a result of cyclin D1 overexpression; p53 signalling, possibly as a consequence of MDM2 overexpression; and the P13K/AKT and mitogen-activated protein kinase/extracellular signal-related kinase pathway pathways that are disturbed as a result of PTEN and GNAQ/11 mutations, respectively. Characteristic chromosomal abnormalities are common and include 6p gain, associated with a good prognosis, as well as 1p loss, 3 loss, and 8q gain, which correlate with high mortality. These are identified by techniques such as fluorescence in situ hybridisation, comparative genomic hybridisation, microsatellite analysis, multiplex ligation-dependent probe amplification, and single-nucleotide polymorphisms. UM can also be categorised by their gene expression profiles as class 1 or class 2, the latter correlating with poor survival, as do BRCA1-associated protein-1 (BAP1) inactivating mutations. Genetic testing of UM has enhanced prognostication, especially when results are integrated with histological and clinical data. The identification of abnormal signalling pathways, genes and proteins in UM opens the way for target-based therapies, improving prospects for conserving vision and prolonging life.

Genetics of primary intraocular tumors

Primary intraocular neoplasms are tumors that originate within the eye. The most common malignant primary intraocular tumor in adults is uveal melanoma and the second is primary intraocular lymphoma or vitreoretinal (intraocular) lymphoma. The most common malignant intraocular tumor in children is retinoblastoma. Genetics plays a vital role in the diagnosis and detection of ocular tumors. In uveal melanoma, monosomy 3 is the most common genetic alteration and somatic mutations of BAP1, a tumor suppressor gene, have been reported in nearly 50% of primary uveal melanomas. The retinoblastoma gene RB1 is the prototype tumor suppressor gene-mutations in RB1 alleles lead to inactivated RB protein and the development of retinoblastoma. Immunoglobulin heavy chain (IgH) or T-cell receptor (TCR) gene rearrangement is observed in B-cell or T-cell primary vitreoretinal lymphoma, respectively. Other factors related to the genetics of these three common malignancies in the eye are discussed and reviewed.

Second malignancies among elderly survivors of cancer

The U.S. population is aging, life expectancy is increasing, and cancer is a disease associated with aging. Advances in screening and therapeutics have led to a growing number of cancer survivors who are at risk for the development of secondary malignancies. Although the risks for the development of second malignancies following a first diagnosis of cancer are well described for survivors of childhood malignancies, there are fewer data for malignancies common in older adults. With the aging of the U.S. population, and with improving survival statistics in many adult malignancies, there is an increasing need to identify those second malignancies that might develop in the older adult survivor of cancer. In this paper, we describe the types and rates of second malignancies following cancers commonly seen in older adults and review the literature on these malignancies. Comparisons are made between older and younger adults with regard to the risks for developing treatment-related cancers with different modalities. Recommendations for early detection of second malignancies are summarized, though there remains an unmet need for evidence-based guidelines for screening for second malignancies in the older adult in particular.

Germline BAP1 mutations predispose to malignant mesothelioma

Because only a small fraction of asbestos-exposed individuals develop malignant mesothelioma¹, and because mesothelioma clustering is observed in some families¹, we searched for genetic predisposing factors. We discovered germline mutations in BAP1 (BRCA1-associated protein 1) in two families with a high incidence of mesothelioma. Somatic alterations affecting BAP1 were observed in familial mesotheliomas, indicating biallelic inactivation. Besides mesothelioma, some BAP1 mutation carriers developed uveal melanoma. Germline BAP1 mutations were also found in two of 26 sporadic mesotheliomas: both patients with mutant BAP1 were previously diagnosed with uveal melanoma. Truncating mutations and aberrant BAP1 expression were common in sporadic mesotheliomas without germline mutations. These results reveal a BAP1-related cancer syndrome characterized by mesothelioma and uveal melanoma. We hypothesize that other cancers may also be involved, and that mesothelioma predominates upon asbestos exposure. These findings will help identify individuals at high risk of mesothelioma who could be targeted for early intervention.

GWAS findings for human iris patterns: associations with variants in genes that influence normal neuronal pattern development

Human iris patterns are highly variable. The origins of this variation are of interest in the study of iris-related eye diseases and forensics, as well as from an embryological developmental perspective, with regard to their possible relationship to fundamental processes of neurodevelopment. We have performed genome-wide association scans on four iris characteristics (crypt frequency, furrow contractions, presence of peripupillary pigmented ring, and number of nevi) in three Australian samples of European descent. Both the discovery (n = 2121) and replication (n = 499 and 73) samples showed evidence for association between (1) crypt frequency and variants in the axonal guidance gene SEMA3A (p = 6.6 × 10(-11)), (2) furrow contractions and variants within the cytoskeleton gene TRAF3IP1 (p = 2.3 × 10(-12)), and (3) the pigmented ring and variants in the well-known pigmentation gene SLC24A4 (p = 7.6 × 10(-21)). These replicated findings individually accounted for around 1.5%-3% of the variance for these iris characteristics. Because both SEMA3A and TRAFIP1 are implicated in pathways that control neurogenesis, neural migration, and synaptogenesis, we also examined the evidence of enhancement among such genes, finding enrichment for crypts and furrows. These findings suggest that genes involved in normal neuronal pattern development may also influence tissue structures in the human iris.

Uveal and Conjunctival Malignant Melanoma in Denmark, 1943–97: Incidence and Validation Study

PURPOSE

To study the incidence of malignant melanoma in the ocular region in Denmark during the period 1943-97.

METHODS

The patients were mainly identified through the Danish Cancer Registry. Age-period-cohort modelling of the incidence rates was done based on age at diagnosis, calendar period and birth cohort in 5-year groups and for each gender.

RESULTS

The age-standardized incidence of malignant melanoma in the ocular region was 0.78 for men (N = 1327) and 0.65 for women (N = 1242) per 100,000 person-years. Calendar period and birth cohort had no effect on the incidence in the ocular region or in the topography subgroups choroid/ciliary body and conjunctiva. However, the incidence increased with birth cohort for iris melanomas.

CONCLUSIONS

The incidence of malignant melanoma in the ocular region was stable in contrast to a major increase in cutaneous melanoma in Denmark during the period 1943-97. The incidence of iris melanomas increased substantially, whereas the rate was stable for choroid/ciliary body and conjunctival melanomas.

Phenotypical characteristics, lifestyle, social class and uveal melanoma

PURPOSE

To investigate potential risk factors of uveal melanoma, including phenotypical characteristics, eye burns, social class, smoking and alcohol consumption.

METHODS

A hospital-based and population-based case-control study of uveal melanoma was carried out from 1995 through 1998 and the results pooled. A total of 118 patients (59 men and 59 women) with uveal melanoma and 475 controls matching on sex, age and study regions were interviewed. Conditional logistic regression was used to calculate odds ratios (OR) and 95% confidence intervals (95% CI).

RESULTS

There was an elevated risk for blue or grey iris color (OR = 3.0, 95% CI 1.5-6.0). Red or blond hair color at age 20 was slightly associated with an increased risk for uveal melanoma (OR = 1.5, 95% CI 0.9-2.4). There was no elevated risk for a history of eye burns (OR = 1.1, 95% CI 0.5-2.4).

CONCLUSIONS

Among the potential risk factors studied, only the phenotypical characteristics showed an association with the risk of uveal melanoma.

Malignant melanoma of the conjunctiva in children: a review of the international literature 1965-2006

PURPOSE

Conjunctival melanoma is rare in children. This article presents a comprehensive review and discusses the clinical significance of the published cases of malignant melanoma of the conjunctiva in children younger than 15 years.

MATERIALS AND METHODS

To obtain prior reports of conjunctival melanoma in children, a systematic search of the world literature was conducted. Additional studies were identified from the bibliographies of the retrieved articles, as well as from major ophthalmic textbooks.

RESULTS

A review of the literature resulted in 28 reported cases of conjunctival melanoma in children younger than 15 years, and only 8 had adequate case details.

CONCLUSION

Malignant melanoma of the conjunctiva is a rare condition in children. Limited knowledge for management and prognosis of this condition in children is largely due to its low occurrence.

Familial risks for eye melanoma and retinoblastoma: results from the Swedish Family-Cancer Database

No systematic population-based studies have been conducted on familial eye cancers. Reliable data on familial risks are important for clinical counselling and cancer genetics. The current analysis was based on the nation-wide Swedish Family-Cancer Database on 10.5 million individuals, containing families with parents and offspring. Cancer data were retrieved from the Swedish Cancer Registry from the years 1958 to 2002, including 3636 patients with any type of eye cancer. Familial risk for offspring was defined using the standardized incidence ratio (SIR), adjusted for many variables. Ocular melanoma was detected in two parent-offspring pairs, but the SIR of 3.90 was not significant. Parental upper aerodigestive tract (2.05), left-sided colon (1.83) and male non-medullary thyroid (6.98) cancers showed an association with ocular melanoma, albeit some with a borderline significance. The SIR for leukaemia was increased when parents were diagnosed with eye melanoma. There was no evidence for the association of ocular melanoma with cutaneous melanoma. The SIR for ocular melanoma was 1.76 when a sister was diagnosed with breast cancer, but there was no increase when a mother was diagnosed with breast cancer. When both a child and the parent presented with retinoblastoma, the SIR was 900. The parents of children with retinoblastoma had an excess of small intestinal and rectal cancers and Hodgkin's disease. The present findings were based on a limited number of cases, but they display a complex and heterogeneous pattern of familial associations in ocular melanoma, including an association with breast cancer through a putative recessive mechanism.

Les mélanocytes choroïdiens normaux et malins : de la cellule à la clinique

The molecular and cellular basis of human choroidal malignant melanoma progression has remained largely unknown. However, choroidal melanoma is the most important primary intraocular tumor in adults. Developmentally, choroidal melanocytes are of neural crest origin similar to cutaneous melanocytes. However, there are some significant differences between cutaneous and uveal melanocytes that have yet to be fully assessed. The purpose of this study is to describe choroidal melanocytes. We will describe the significant differences between cutaneous and uveal melanocytes as well as the congenital and acquired diseases of uveal melanocytes. We will then describe the cellular and molecular mechanisms involved in melanoma progression.

Incidence of noncutaneous melanomas in the U.S

BACKGROUND

Description of the epidemiology of noncutaneous melanoma has been hampered by its rarity. The current report was the largest in-depth descriptive analysis of incidence of noncutaneous melanoma in the United States, using data from the North American Association of Central Cancer Registries.

METHODS

Pooled data from 27 states and one metropolitan area were used to examine the incidence of noncutaneous melanoma by anatomic subsite, gender, age, race, and geography (northern/southern and coastal/noncoastal) for cases diagnosed between 1996 and 2000. Percent distribution by stage of disease at diagnosis and histology were also examined.

RESULTS

Between 1996 and 2000, 6691 cases of noncutaneous melanoma (4885 ocular and 1806 mucosal) were diagnosed among 851 million person-years at risk. Ocular melanoma was more common among men compared with women (6.8 cases per million men compared with 5.3 cases per million women, age-adjusted to the 2000 U.S. population standard), whereas mucosal melanoma was more common among women (2.8 cases per million women compared with 1.5 cases per million men). Rates of ocular melanoma among whites were greater than eight times higher than among blacks. Rates of mucosal melanoma were approximately two times higher among whites compared with blacks.

CONCLUSIONS

In contrast to cutaneous melanoma, there was no apparent pattern of increased noncutaneous melanoma among residents of southern or coastal states, with the exception of melanoma of the ciliary body and iris. Despite their shared cellular origins, both ocular and mucosal melanomas differ from cutaneous melanoma in terms of incidence by gender, race, and geographic area.

Case-control study on uveal melanoma (RIFA): rational and design

Background

Although a rare disease, uveal melanoma is the most common primary intraocular malignancy in adults, with an incidence rate of up to 1.0 per 100,000 persons per year in Europe. Only a few consistent risk factors have been identified for this disease. We present the study design of an ongoing incident case-control study on uveal melanoma (acronym: RIFA study) that focuses on radiofrequency radiation as transmitted by radio sets and wireless telephones, occupational risk factors, phenotypical characteristics, and UV radiation.

Methods/Design

We conduct a case-control study to identify the role of different exposures in the development of uveal melanoma. The cases of uveal melanoma were identified at the Division of Ophthalmology, University of Essen, a referral centre for tumours of the eye. We recruit three control groups: population controls, controls sampled from those ophthalmologists who referred cases to the Division of Ophthalmology, University of Duisburg-Essen, and sibling controls. For each case the controls are matched on sex and age (five year groups), except for sibling controls. The data are collected from the study participants by short self-administered questionnaire and by telephone interview. During and at the end of the field phase, the data are quality-checked.

To estimate the effect of exposures on uveal melanoma risk, we will use conditional logistic regression that accounts for the matching factors and allows to control for potential confounding.

Ocular melanoma

This article reviews the current pathogenesis, molecular changes, diagnosis, and treatment of ocular melanomas. Ocular melanomas can involve the eyelid, conjunctiva, intraocular structures, and the orbit. The most common eye melanoma involves the uveal tract and is responsible for approximately 13% of melanoma deaths. Uveal melanomas account for 10% of all melanomas.

BRCA2 mutations in a population-based series of patients with ocular melanoma

We studied the BRCA2 gene for germline mutations in 71 of 99 patients (72%) with ocular melanoma who were diagnosed consecutively in Australia in 1997 and 1998. Patients considered for our study fulfilled one of the following critiera: (i) were 50 years of age or less at diagnosis; (ii) had bilateral disease (2 patients); (iii) reported a family history of ocular melanoma (4 patients). Mutation detection was performed using the protein truncation test and denaturing high-performance liquid chromatography with primers designed to include intron-exon boundaries. Six DNA changes were found of which 2 were exonic, in exons 14 (A>C in nucleotide 7244 leading to His>Arg) and 27 (base pair substitution in nucleotide 9976 leading to a stop codon). One exonic change has been reported previously. None of the intronic mutations were deemed to affect splicing efficiency. Neither exonic mutation was in a person with bilateral ocular melanoma or a family history of cutaneous melanoma. We estimated the prevalence of possible loss of function changes in BRCA2 in patients with ocular melanoma at 3% (95% CI 0-10%). This figure was similar to previous estimates of 2.8% and 2% in nonrepresentative samples of patients with ocular melanoma and 2.1% in a representative sample of young women with breast cancer.

Genetics of familial and sporadic melanoma

Like many other cancers, melanoma has a significant genetic basis. However, its genetic pathways may involve multiple genes with probable interactions with sun exposure. Germline mutations in p16 or CDKN2A are found in a significant percentage of relatively rare melanoma families but p16 mutations are uncommon in sporadic tumours. p16 may still be involved by other mechanisms of inactivation; however, it is clear that other melanoma genes remain to be discovered. Family, case-control, twin and sib-pair analyses as well as DNA chip technology may shed some light on genes involved in melanocytic differentiation and skin pigmentation. Recent public health campaigns have not been very successful in changing behaviour regarding tanning, and the relationship between sun exposure and melanoma is very complex. With the understanding of genetic alterations leading to this tumour, follow-up strategies and behavioural interventions may be more specifically designed to target high risk groups.